Results for "Reference"
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MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It does not compute the alignments explicitly, but...Tags: MashMap, fast, approximate, software, mapping, long, reads, PacBio, ONT, assembly, reference, genome(s)
2330 days ago
Carefully opt for human reference genome
Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference genome. if you map reads to GRCh38 or hg38, use the following: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/00...Tags: Carefully, opt, human, reference, genome
1532 days ago
pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with Quiver if --forQuiver optio...Tags: pbalign, maps, PacBio, reads, reference, sequences, alignments, BAM, NGS
2167 days ago
- Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter problems Optional: Gzip the delta file to speed up upload (usually 2-4X f...
Tags: assemblytics, delta, analyze, alignment, assembly, reference, genome, visualization
2146 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called red-black multipositional de Bruijn graph to detect...Tags: ReMILO, reference, assisted, misassembly, detection, algorithm, short, long, reads
2124 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of: Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together. Reducing/removing reference bias as compared to mapping...Tags: ARC, pipeline, facilitates, iterative, reference, guided, de novo, assemblies
2104 days ago
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